Hello all, when running preproc-sess, I got this error message: ERROR: could not determine file for /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain Try running mkbrainmask-sess with -per-run
I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d . -fsd bold m) and got the output below, which shows a problem with a shared library?
Any suggestions?
Corinna
------------------------------------------------ /usr/local/freesurfer/subjects/symmetry/lindsay/first_test Fri Apr 12 15:53:14 EDT 2013 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_9634 /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996119, -0.0108587, 0.0873391) j_ras = (0.000562893, 0.991553, 0.129698) k_ras = (0.0880098, -0.129244, 0.9877) writing to /tmp/mkbrainmask_9634/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f 0.1 /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o /tmp/mkbrainmask_9634/brain_mask.nii sysname Linux hostname lotfi machine x86_64 user bauer
input /tmp/mkbrainmask_9634/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_9634/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0